Syllabus

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Sep 8

The rise, fall, and rise of history

Ch. 1, Brooks and McLennan
Ch. 1, Pagel and Harvey

 

Sep 12

Phylogenetic reconstruction

Ch. 2, Brooks and McLennan

Ch. 3, Harvey and Pagel

Sep 15

More phylogenetic reconstruction

Ch 9. Brooks and McLennan

Sep 19

Practice Session for reconstruction

 

Sep 22

Speciation

Ch 3, Ch. 4; Brooks and McLennan

Sep 26

Speciation readings

 

Mendelson and Shaw.  2005. Nature

Shaw.  2002. PNAS

Richman.  1996.  Evolution

Sep 29

Diversification

pp 127-132, Ch. 4; Brooks and McLennan

pp. 1-21, Ch. 1; Harvey and Pagel

Oct 3

Diversification Readings

 

Nee.  2004. Paleobiology

Davies et al.  2004.  Proceedings of the Royal Society of London

Davies et al.  2004.  PNAS 

Oct 6

Adaptation

pp 133-169, Ch. 5; Brooks and McLennan

Mace et al. 2003.  Comparative Biochemistry and Physiology Part A.

Oct 10

Adaptation Readings

pp 22-34, Ch. 1; Harvey and Pagel   

Perez-Barberia.  2001.  Oecologica.  

Oct 13

Limitations to the comparative approach

Ch. 2, Harvey and Pagel, pp.164-169

Ch. 5; Brooks and McLennan

Leroi et al.  1994. The American Naturalist

Oct 17

Discrete Characters

Ch. 4, Harvey and Pagel

Ronquist.  2004.  TREE

Oct 20

MacClade Session I*

Reading: Manual (Ch. 1 and 2)

Meet in ESB 103

Oct 24

MacClade Session II and Mesquite*

Reading: Mesquite Manual

Meet in ESB 103 Note special meeting time:  7-9

Oct 27

Mesquite*

Meet in ESB 103

Oct 31

Quantitative (continuous) character states

Ch. 5., Harvey and Pagel

Felsenstein.  1985.  The American Naturalist

Issac et al.  2003. Evolution

Nov 3

CAIC Session*

Reading: Manual

New info for v 2.6

Meet in ESB 103

Nov 7

Cactus Session*

Reading: Manual

Meet in ESB 101

Nov 10

Quantitative character Readings I

Webster and Purvis.  2002.  Proceedings of the Royal Society of London   

Linder.  2000.  The American Naturalist

Nov 14

Quantitative character Readings II

Butler and King.  2004.  The American Naturalist

Oakley and Cunningham.  2000.  Evolution

Nov 17

Adaptive radiations

pp 170-188, Ch. 5, Brooks and McLennan

Joyce et al.  2005.  Nature

Kozak et al.  2005.  Evolution

Nov 21

Co-speciation Co-adaptation

Ch 6, Ch 7 Brooks and McLennan

Stevens.  2004.  Briefings in Bioinformatics

Nov 24

Thanksgiving (class only if necessary ;-)

Special reading

Nov 28

Co-adaptation reading

Koene and Schulenberg.  2005.  BMC Evolutionary Biology

Weiblen.  2004.  Systematic Biology

Dec 1 Coevolution Ch 8 Brooks and McLennan

Dec 5

Presentation of results from analyses

 

Dec 8

Presentation of results from analyses

 

*These meetings will be for computer labs.  Be sure to note the room that the session will be in.  Also note that the Oct. 24 meeting will be at a different time!

 

 

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